tbuckley/cabot-search huggingface dataset:
Abstract B035: Targeting ribosome biogenesis addition is a novel strategy for pancreatic cancer therapy
Authors: Mudassier Ahmad, Carlos Perez, Andrew Massey, Vivek Kashyap, Neeraj Chauhan, Haider Ahsan, Jasmine Jasmine, Manish Tripathi, Subhash Chauhan, Bilal Hafeez
Journal: Cancer Research (2022)

Abstract Pancreatic cancer (PanCa) is the third leading cause of cancer-related deaths in the United States with limited therapeutic options available. Gemcitabine (GEM), a deoxycytidine nucleoside analog is currently considered the most effective therapy for PanCa; however, it shows only a marginal survival benefit of 6 months. PanCa cells are addicted to ribosome biogenesis (RiBi) which supports their high rate of growth and proliferation. Therefore, strategically targeting the process of RiBi could be one of the ideal strategies for the prevention and treatment of PanCa. In this study, we for the first-time report that RPA194, a catalytic subunit of RNA Pol I is differentially expressed in normal pancreatic ductal epithelial (NPDE) and cancer cells. We also observed differential expression of RPA194 in various grades of pancreatic tumor tissues and its level was increased in high-grade pancreatic tumor tissues. We tested our hypothesis that targeting RPA194 with a non-toxic pharmacological inhibitor (BMH-21) will inhibit the growth of advanced PanCa. We observed that BMH-21 inhibits the growth and induced apoptosis of PanCa cells in a dose-dependent manner and this inhibition was correlated with the expression of RPA194. We observed proteasomal mediated degradation of RPA194 in PanCa cells. BMH-21 treatment inhibited RPA194 occupancy on rDNA but did not affect other nucleolar proteins (UBF, fibrillarin, nucleolin, and nucleophosmin). Two times the effective concentration of BMH-21 (5 µM) did not show any cytotoxic effect in NPDE cells. However, BMH-21 degraded RPA 194 protein in these cells in a similar manner as in PanCa cells. Therefore, we speculate that other proteins are involved in the selective toxicity of BMH-21 in PanCa cells. These findings were translated to in vivo model systems. We observed that BMH-21 significantly (P&amp;lt;0.01) inhibited the growth of pancreatic tumors in an orthotopic xenograft model. This pancreatic tumor growth inhibition was correlated with degradation of RPA194 protein in BMH-21 treated mice tumor tissues followed by inhibition of cell proliferation markers (ki67 and PCNA). Taken together, our results strongly suggest that targeting the RiBi process is a novel approach and BMH-21 is a non-toxic potential targeting agent for the prevention and treatment of advanced PaCa. Citation Format: Mudassier Ahmad, Carlos Perez, Andrew Massey, Vivek Kashyap, Neeraj Chauhan, Haider Ahsan, Jasmine Jasmine, Manish Tripathi, Subhash Chauhan, Bilal Hafeez. Targeting ribosome biogenesis addition is a novel strategy for pancreatic cancer therapy [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B035.
Abstract A004: Repetitive elements and viral mimicry co-evolve in pancreatic cancer
Authors: Siyu Sun
Journal: Cancer Research (2022)

Abstract Overexpression of repetitive DNA is an emerging hallmark of human cancers and several repeats, such as SINE elements and satellite, transcribe immunostimulatory RNA that mimic features associated with viral infection. However, the extent to which specific repeat families affect tumor evolution and the immune microenvironment in a pro-or anti-tumorigenic manner remains poorly understood. We present an integrated, evolutionary multi-omic analysis pf repeat evolution in multiregion-sampled human metastatic and primary pancreatic cancers for the first time. We found that LINE-1 (L1) somatic insertion location coincides with tumor evolution. Moreover, we found L1 activity is negatively correlated with immunogenic SINE element expression. Two orthogonal metrics were used in quantifying immunogenicity of SINE elements: IFN signature and capability of forming dsRNA, where both methods revealed that evolutionary young SINE elements have stronger correlation with IFN signatures and are more likely to form dsRNAs. Moreover, the anti-correlation between L1 activity and SINE expression is validated through both immunohistological analysis of human samples and pancreatic cancer cell lines. In the end, we proposed that the model of hypoactive L1 is beneficial for tumors by suppression of immunogenic SINE elements through either their direct reverse transcription or accelerating their degradation. Our analysis therefore sheds light on the evolutionary role of dark matter repeats in a tumor’s adaptation to immunogenic vulnerabilities. Citation Format: Siyu Sun. Repetitive elements and viral mimicry co-evolve in pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr A004.
Abstract B045: Evaluating the role of altered RNA metabolism in pancreatic cancer therapy resistance
Authors: Md Afjalus Siraj, Xinning Shan, Robert Tseng, Luisa Escobar-Hoyos
Journal: Cancer Research (2022)

Abstract Pancreatic ductal adenocarcinomas (PDACs) are highly lethal, mostly because they quickly develop resistance to current chemotherapies: Gemcitabine (GEM)/paclitaxel or cocktail FOLFIRINOX. Both chemotherapies rely on nucleoside analogues (GEM and 5-fluorouracil [5-FU], and resistance is developed without acquiring mutations, suggesting the role of non-mutational mechanisms for therapy resistance. Our recent findings demonstrated that PDACs depend on RNA splicing proteins to maintain tumors and are exquisitely susceptible to a range of therapies directed at RNA splicing, supporting the role of aberrant RNA splicing in PDAC therapy resistance. Here we evaluated the role of altered RNA splicing in PDAC therapy resistance. Three murine and human isogenic lines with either sensitivity or resistance to GEM were developed. We performed deep RNA sequencing (RNASeq, 80-100 million reads, traditional is 20-40 million reads), differential gene expression, and splicing analyses. GEM resistant PDAC cells demonstrated &amp;gt;40% of non-canonical RNA splice variants and altered expression of 30% of RNA-binding proteins encoded in the human/murine genome, compared to GEM sensitive ones. Specific alternatively spliced exons with common cis-elements were identified in therapy resistant cells, suggesting that these splicing changes are guided by a splicing factor or other RNA-binding protein(s) (RBPs). Top splicing changes were associated to mRNAs encoding ether lipid and pyruvate metabolism. This finding is important as previous studies have linked these metabolic pathways to therapy resistance, however, they have overlooked if protein isoforms, resulting from aberrant splicing, have different impacts in therapy resistance. In addition, GEM and H3B-8800, a novel spliceosome inhibitor showed higher synergistic activity in GEM resistant PDAC cells compared to GEM sensitive cells, suggesting that the development of resistance in PDAC is highly dependent on RNA splicing. Combinedly, these data strongly suggest that resistance to chemotherapeutic agents in PDAC cells requires altered RNA splicing and aberrant expression of associated proteins. Further investigation is ongoing to identify the splicing events and RBPs related to chemotherapy resistance, which will uncover novel mechanisms of therapy resistance and therapeutic modalities by targeting RNA splicing in pancreatic cancer. Citation Format: Md Afjalus Siraj, Xinning Shan, Robert Tseng, Luisa Escobar-Hoyos. Evaluating the role of altered RNA metabolism in pancreatic cancer therapy resistance [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B045.
Abstract B023: RHAMMB promotes pancreatic cancer metastasis
Authors: Xiang Chen, Tiantian Zhang, Seung Koo Lee, Dunrui Wang, Zhengming Chen, Ching-Hsuan Tung, Yao-Tseng Chen, Yi-Chieh Nancy Du
Journal: Cancer Research (2022)

Abstract Pancreatic cancer is a leading cause of cancer-related death. The most common type of pancreatic cancer is pancreatic ductal adenocarcinoma (PDAC), and pancreatic neuroendocrine tumor (PNET) is the second common malignancy of pancreas. Pancreatic cancer patients are often diagnosed with metastatic diseases. The 5-year survival is lowest for pancreatic cancer among all cancers. There is an urgent need to understand the key regulators for pancreatic cancer metastasis and develop new therapeutic strategies. We found that Receptor for hyaluronan-mediated motility (RHAMM) is overexpressed in pancreatic cancer, but it is absent or limited in normal human tissues and not expressed in adult pancreas. RHAMM was initially identified as a protein that binds to hyaluronic acid (HA). RHAMM promotes HA-induced motility, modulates cytoskeletal organization, and activates extracellular-regulated kinase (Erk). RHAMM encodes 18 exons and alternative splicing yields different isoforms, RHAMMv1-4. We found that RHAMMB (known as RHAMMv3) is the most prominent alternative splicing isoform in PDAC and PNET, and high RHAMMB mRNA levels correlate with inferior survival of pancreatic cancer patients in TCGA cohort. We demonstrated that RHAMMB overexpression promotes metastasis of pancreatic cancer in mouse models and knockdown of RHAMM by shRNA suppresses migration and metastasis. Given RHAMM’s tumor-specific overexpression patten, we developed nanoparticles to target RHAMMB-overexpressing pancreatic cancer. We demonstrated that RHAMM-targeting nanoparticles loaded with multiple therapeutics can be used as a systemic therapy to suppress RHAMMB-overexpressing tumors in immunocompetent mice. Taken together, RHAMMB plays an important role for pancreatic cancer metastasis and serves as a therapeutic gateway for pancreatic cancer treatment. Citation Format: Xiang Chen, Tiantian Zhang, Seung Koo Lee, Dunrui Wang, Zhengming Chen, Ching-Hsuan Tung, Yao-Tseng Chen, Yi-Chieh Nancy Du. RHAMMB promotes pancreatic cancer metastasis [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B023.
Abstract B062: Activation of the MAPK pathway by altered RNA splicing in cancer
Authors: Yushan Zhang, Md Afjalus Siraj, Prabir Chakrabarty, Robert Tseng, Shamik Das, Resham Bhattacharya, Luisa Escobar-Hoyos, Priyabrata Mukherjee
Journal: Cancer Research (2022)

Abstract Many cancers carry recurrent, change-of-function mutations affecting RNA splicing factors, however, less is known about the consequences of upregulated RNA splicing factors (SFs) in cancer. Here, we describe a role of survival motor neuron domain containing 1 (SMNDC1) protein, a poorly studied SF that we found to be upregulated in pancreatic ductal adenocarcinoma (PDAC) and high-grade serous ovarian cancers (HGSOCs) and associated with poor patient prognosis. By loss- and gain-of- function approaches we found that SMNDC1 promotes cancer cell proliferation, clonal expansion and tumor growth. Mechanistically, SMNDC1 promoted the retention of A/C-rich exons which otherwise would be excluded or less retained after RNA splicing in normal cells. Inclusion of exon 4 (E4) of MAPK3 (ERK1), which encodes both phosphorylation sites (Thr202/Tyr204) of the kinase, was among the promoted exons by SMNDC1. Forced exclusion of MAPK3 E4 using anti-sense oligos in vitro and in vivo, inhibited the phosphorylation of ERK1/2, the expression of downstream genes (Cyclin D1, Elk1) and increased proapoptotic proteins. These data provide a novel mechanism by which PDAC and HGSOC cells exploit a “splicing switch” that increases ERK1 phosphorylation, and offer a druggable alternative to target these cancer cells by jointly blocking oncogenic signaling and altered RNA splicing. Citation Format: Yushan Zhang, Md Afjalus Siraj, Prabir Chakrabarty, Robert Tseng, Shamik Das, Resham Bhattacharya, Luisa Escobar-Hoyos, Priyabrata Mukherjee. Activation of the MAPK pathway by altered RNA splicing in cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B062.
Abstract B041: DCLK1 isoforms 2 and 4 c-terminal extracellular binding domain mediates PDAC tumorigenesis through protein-protein interactions
Authors: Parthasarathy Chandrakesan, Landon Moore, Randal May, Kamille Pitts, Edwin Bannerman-Menson, Milton Brown, Courtney Houchen
Journal: Cancer Research (2022)

Abstract Doublecortin-like kinase 1 (DCLK1) plays a major role in tumor initiation, progression, and metastasis of solid tumors including pancreatic ductal adenocarcinoma (PDAC). Elevated expression of DCLK1 in patient tumors leads to poor overall survival, however, the precise mechanisms that regulate the pro-tumorigenic functions of DCLK1 continue to be explored. We have reported that the proprietary monoclonal antibody, CBT-15, binds to the C-terminal extracellular domain of DCLK1 isoforms 2/4 in PDAC and treatment with CBT-15 resulted in tumor xenograft growth arrest in PDAC and reduced tumor growth in the KPC mouse model of PDAC. To determine the functional activity of the DCLK1 isoform 2/4 extracellular domain and CBT-15 action, we screened a peptide library against DCLK1 isoform 4 and identified eight peptides that bound to the C-terminal extracellular domain. In this study, we evaluated the biological impact of these peptides on colony and spheroid formation using AsPC-1 and Capan-1 pancreatic cancer cell lines. We found a greater than 90% reduction in spheroid formation compared to vehicle control for Capan-1 cells treated with peptide #1 (1 μM). Furthermore, peptide #1 treatment of AsPC-1 cells derived mouse xenografts resulted in a greater than 65% reduction in xenograft growth (P-value &amp;lt; 0.01, 10 mg/kg, i.p.). This highly active peptide binds the extracellular domain with 60% inhibition at 50 nM determined by SPR and has a Kd of 30±10 nM. To identify potential DCLK1 extracellular domain binding partners, we developed an algorithm that identified five proteins that are key regulators of tumorigenesis and exhibit structural characteristics that would allow for binding to the DCLK1 extracellular domain. Further work is focused on confirming the interactions between DCLK1 extracellular domain and candidate targets as well as whether peptide #1 blockade of protein-protein interactions disrupts pro-tumorigenic functions of DCLK1. Citation Format: Parthasarathy Chandrakesan, Landon Moore, Randal May, Kamille Pitts, Edwin Bannerman-Menson, Milton Brown, Courtney Houchen. DCLK1 isoforms 2 and 4 c-terminal extracellular binding domain mediates PDAC tumorigenesis through protein-protein interactions [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B041.
Abstract B078: PP2A activation drives alternative EGFR activation in PDAC
Authors: Claire M. Pfeffer, Sydney J. Clifford, Elizabeth G. Hoffman, Gagan K. Mall, Garima Baral, Brittany L. Allen-Petersen
Journal: Cancer Research (2022)

Abstract Pancreatic ductal adenocarcinoma (PDAC) stands to become the 2nd most deadly cancer by 2030. Over 90% of PDAC patients have oncogenic KRAS mutations with the most prevalent being KRASG12D which have proven difficult to therapeutically target. Several studies have implicated EGFR signaling as critical for PDAC tumorigenesis in KRAS mutant tumors. Consistent with these findings, the first FDA-approved targeted therapeutic for PDAC was the EGFR inhibitor, Erlotinib. However, single agent use of Erlotinib has shown minimal efficacy in the clinic suggesting that this signaling is complex and needs further interrogation. Studies have shown the serine/threonine phosphatase, Protein Phosphatase 2A (PP2A), negatively regulates several downstream targets of EGFR and KRAS. Our previous studies using small molecule activators of PP2A demonstrate a heterogeneous response to PP2A activation, with some PDAC cell lines downregulating oncogenic signals and others maintaining the oncogenic signaling. Using pharmacological activation of PP2A, as well as overexpression and knockdown studies, we have identified a novel signaling cascade in which PP2A activation leads to increased expression and secretion of EGFR ligands and EGFR activation in a subset of PDAC cell lines. Given this unique feedback mechanism, we combined EGFR inhibitors with PP2A activation and found that the combination killed more cells than either agent alone. Together, our studies identify a novel role for PP2A in regulating EGFR signaling and support the combined use of EGFR inhibitors and PP2A activators to increase efficacy of both agents. Citation Format: Claire M. Pfeffer, Sydney J. Clifford, Elizabeth G. Hoffman, Gagan K. Mall, Garima Baral, Brittany L. Allen-Petersen. PP2A activation drives alternative EGFR activation in PDAC [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B078.
Abstract C043: Addition of losartan to FOLFORINOX and chemoradiation downregulates pro-invasion and immunosuppression-associated genes in locally advanced pancreatic cancer
Authors: Yves Boucher, Jessica M. Posada, Sonu Subudhi, Spencer R. Rosario, Liqun Gu, Ashwin S. Kumar, Heena Kumra, Mari Mino-Kenudson, Nilesh P. Talele, Dan G. Duda, Dai Fukumura, Jennifer Y. Wo, Jeffrey W. Clark, David P. Ryan, Carlos Fernandez-Del Castillo, Theodore S. Hong, Mikael J. Pittet, Rakesh K. Jain
Journal: Cancer Research (2022)

Abstract Purpose: Adding losartan to FOLFIRINOX (FFX) chemotherapy followed by chemoradiation (CRT) resulted in 61% R0 surgical resection in our phase II trial in patients with locally advanced pancreatic cancer. Here we identify potential mechanisms of benefit by assessing the effects of neoadjuvant losartan+FFX+CRT versus FFX+CRT on the stromal tumor microenvironment. Experimental Design: We performed a gene expression analysis of RNA extracted from pancreatic cancer tissue sections and immunofluorescence for cancer cells and immune cells using archived surgical samples from patients treated with losartan+FFX+CRT (NCT01591733), FFX+CRT (NCT01591733) or surgery upfront, without any neoadjuvant therapy. We then assessed whether certain gene sets could stratify the overall survival of patients. Results: Neoadjuvant losartan+FFX+CRT and FFX+CRT increased the expression of genes linked to vascular normalization, transendothelial migration of leukocytes, T cell activation and cytolytic activity, and dendritic cell related genes versus no neoadjuvant treatment. In comparison to FFX+CRT, losartan+FFX+CRT downregulated pro-invasion, immunosuppression, and M2 macrophages related genes, and upregulated genes associated with tumor suppression, including the p53 pathway. Furthermore, immunostaining revealed significantly less residual disease in lesions treated with losartan+FFX+CRT versus FFX+CRT. Losartan+FFX+CRT also reduced CD4+FOXP3+ regulatory T cells in pancreatic cancer lesions with a complete/near complete response. Overall survival was associated with dendritic cell and antigen presentation genes for patients treated with FFX+CRT, and with immunosuppression and invasion genes or dendritic cell- and blood vessel-related genes for those treated with losartan+FFX+CRT. Conclusions: Adding losartan to FFX+CRT reduced pro-invasion and immunosuppression related genes, which were associated with improved treatment outcomes in patients with locally advanced pancreatic cancer. Citation Format: Yves Boucher, Jessica M. Posada, Sonu Subudhi, Spencer R. Rosario, Liqun Gu, Ashwin S. Kumar, Heena Kumra, Mari Mino-Kenudson, Nilesh P. Talele, Dan G. Duda, Dai Fukumura, Jennifer Y. Wo, Jeffrey W. Clark, David P. Ryan, Carlos Fernandez-Del Castillo, Theodore S. Hong, Mikael J. Pittet, Rakesh K. Jain. Addition of losartan to FOLFORINOX and chemoradiation downregulates pro-invasion and immunosuppression-associated genes in locally advanced pancreatic cancer [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr C043.
Abstract B036: The role of whole genome duplication in progression of pancreatic ductal adenocarcinoma
Authors: Lauren Hummel, Irene Xie, Karen Ng, Amy Zhang, Stephanie Ramotar, Anna Dodd, Grainne O'Kane, Jennifer Knox, Julie Wilson, Steven Gallinger, Faiyaz Notta
Journal: Cancer Research (2022)

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDA) is a lethal disease that tends to present at an advanced stage, but the evolutionary mechanisms responsible for rapid progression in PDA are poorly understood. Whole genome duplication (WGD) is a hallmark of cancer observed more frequently in late-stage tumors that predicts poorer overall patient survival across cancer types, including PDA. The genome-wide instability that occurs during WGD events can lead to gene dosage imbalances that promote tumor progression and may explain the rapid progression of aneuploidy. Although WGD has been studied extensively in advanced cancer, there is limited data on WGD in primary tumors. We hypothesize that WGD occurs frequently in primary PDA and promotes the rapid progression and high rate of relapse in early stage PDA. We leveraged scWGS to infer copy number profiles and WGD events from tumor cells to determine the rate of subclonal WGD in primary PDA tumors and understand how aneuploidy and genome instability evolve in the earliest stages of tumor progression. Methods: Single cell barcoded libraries from primary treatment naive tumors were prepared with the 10X Genomics Single Cell CNV platform and sequenced to a depth of 20-60x per tumor. Reads were processed using CellRanger DNA pipeline, demultiplexed, and analyzed with Gingko CNV. A total of 10,323 cells from 8 primary PDA tumors (range, 192 – 3146; median = 1286) were recovered, resulting in an average coverage of 0.06x per single cell (range, 0.02x – 0.14x). Results: 5/8 tumors analyzed had evidence of at least one WGD event. The WGD event was identified as a minor subclone in 3 of these 5. Copy number profiles revealed 1-6 distinct subclones in each tumor, demonstrating copy number evolution is ongoing. WGD+ tumors trend towards having higher diversity and higher percentage of genome altered. Conclusion: WGD occurs more frequently in primary PDA than previously understood, and may confer high levels of genetic instability. Citation Format: Lauren Hummel, Irene Xie, Karen Ng, Amy Zhang, Stephanie Ramotar, Anna Dodd, Grainne O'Kane, Jennifer Knox, Julie Wilson, Steven Gallinger, Faiyaz Notta. The role of whole genome duplication in progression of pancreatic ductal adenocarcinoma [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer; 2022 Sep 13-16; Boston, MA. Philadelphia (PA): AACR; Cancer Res 2022;82(22 Suppl):Abstract nr B036.